1. Logical Data Modeling – Attributes, Primary Keys, and Identity
BCHB697

2. Outline The Data Modeling Process Entity Attributes & Types
Determinants and Primary Keys
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3. The Data Modeling Process
Conceptual Data Modeling
Define the entities and their relationships
Logical Data Modeling
Define each entities’ attributes, incl. types
Choose primary key(s) for each entity
Relationship details (cardinality, optional)
Physical Data Modeling
Implementation
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4. Data-Model Properties
Completeness
Non-redundancy
“Business” Logic
Data Reusability
Stability and Flexibility
Elegance
Communication
Integration
Data Modeling Essentials (§1.6)
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5. Entity Attributes Any (and all) details about an entity Person:
Will become columns in database table.
Needs definition and type: string, integer, float, (date,...)
Optional? More than one value?
One fact per attribute, no derivable values, implicit values
Person:
name, family name, date of birth, age, GU ID #, NetID, address, , phone
Course:
course number, department, meeting time(s), day(s), start date, end date, director, syllabus, credits, prerequisites, semester, year
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6. Course Database Attributes
Person:
name, family name, date of birth, age, GU ID #, NetID, address, , phone
Course:
course number, department, meeting time(s), day(s), start date, end date, syllabus, credits, prerequisites, semester, year
CourseParticipant:
person, course, role
BCHB697 - Edwards

7. Blast Database Entities and Attributes
Protein:
accession, gi, species, description, length, (sequence)
Alignment:
bit score, E-value, query protein, reference protein
HighScoringPair:
ordinal, bit score, E-value, identities, positives, gaps, start position, end position, (aligned sequences), query protein, reference protein, (alignment)
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8. Attribute Types Basics: integer, float, string Semantic types:
Sometimes: boolean, date, point (lat, long), …
Missing values of optional attributes: NULL
Multiple values → multiple attributes
Semantic types:
Identifier – unordered, test for equality only
Category – few unordered, discrete values
Numeric – ordered, arithmetic, precision (?)
Text – ordered (sortable), no arithmetic
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9. Course Database Attributes
Person:
name, family name, date of birth, age, GU ID #, NetID, address, , phone
Course:
course number, department, meeting time(s), day(s), start date, end date, syllabus, credits, prerequisites, semester, year
CourseParticipant:
person, course, role
BCHB697 - Edwards

10. Blast Database Entities and Attributes
Protein:
accession, gi, species, description, length, (sequence)
Alignment:
bit score, E-value, query protein, reference protein
HighScoringPair:
ordinal, bit score, E-value, identities, positives, gaps, start position, end position, (aligned sequences), query protein, reference protein, (alignment)
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11. Identifier Attributes
May be integers or strings:
How many identifiers do we need? How many digits/characters in an identifier?
System generated:
Sequential integer automatically generated by the database for each instance.
Administrator assigned:
Manual designation (OK for a few)
Externally defined:
Explicitly provided as entity attribute value
Managed by external organization / authority
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12. Course Database Attributes
Person:
name, family name, date of birth, age, GU ID #, NetID, address, , phone
Course:
course number, department, meeting time(s), day(s), start date, end date, syllabus, credits, prerequisites, semester, year
CourseParticipant:
person, course, role
BCHB697 - Edwards

13. Blast Database Entities and Attributes
Protein:
accession, gi, species, description, length, (sequence)
Alignment:
bit score, E-value, query protein, reference protein
HighScoringPair:
ordinal, bit score, E-value, identities, positives, gaps, start position, end position, (aligned sequences), query protein, reference protein, (alignment)
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14. Determinants
A determinant is any identifier attribute (or set of identifier attributes) of an entity that determines other attributes’ values.
This should be true conceptually, not just for the current set of instances
A candidate key of an entity is a determinant that determines all of the entity’s other attribute values.
BCHB697 - Edwards

15. Course Database Attributes
Person:
name, family name, date of birth, age, GU ID #, NetID, address, , phone
Course:
course number, department, meeting time(s), day(s), start date, end date, syllabus, credits, prerequisites, semester, year
CourseParticipant:
person, course, role
BCHB697 - Edwards

16. Blast Database Entities and Attributes
Protein:
accession, gi, species, description, length, (sequence)
Alignment:
bit score, E-value, query protein, reference protein
HighScoringPair:
ordinal, bit score, E-value, identities, positives, gaps, start position, end position, (aligned sequences), query protein, reference protein, (alignment)
BCHB697 - Edwards

17. Primary Keys
Every entity (that might be referenced) requires one candidate key be designated the primary key.
Surrogate for instance identity
Must be universal, unique, and stable.
Primary key values are used to define entity / instance relationships
Foreign keys are identity attributes with an entity’s primary keys as values.
Single attribute, integer, primary keys are usually best.
BCHB697 - Edwards

18. Course Database Attributes
Person:
name, family name, date of birth, age, GU ID #, NetID, address, , phone
Course:
course number, department, meeting time(s), day(s), start date, end date, syllabus, credits, prerequisites, semester, year
CourseParticipant:
person, course, role
BCHB697 - Edwards

19. Blast Database Entities and Attributes
Protein:
accession, gi, species, description, length, (sequence)
Alignment:
bit score, E-value, query protein, reference protein
HighScoringPair:
ordinal, bit score, E-value, identities, positives, gaps, start position, end position, (aligned sequences), query protein, reference protein, (alignment)
BCHB697 - Edwards

20. Logical data model Entities: Course, Person, CourseParticipant
BCHB594 nje5 rcf57 sg1386 kg737 yk625 yl1009 bm999 ls1340 sls358 ss4218 zsw6
BCHB580 nje5 ker25 sg1386 kg737 bh658 yk625 yl1009 bm999 war36 ls1340 sls358 ss4218 zsw6 mdw83 yw575 my511
BCHB697 nje5 sg1386 bh658 xh61 yk625 yl1009 bm999 ls1340 ss4218 lmw116 zsw6 yw575
Course
course_id department
number
semester
year
Person
person_id name
dob
GU ID #
NetID
CourseParticipant
course_id
person_id role 1 1
course
person
Entities: Course, Person, CourseParticipant
Relationships: Course ← CourseParticipant, Person ← CourseParticipant
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21. Exercise Navigate to a bioinformatics knowledgebase
UniProt, dbSNP, ClinVar, PDB, …
Identify the entities and relationships
Identify the attributes of each entity
Choose a primary key for each entity
Reading: Chapters (4),5,6 (DME)
BCHB697 - Edwards